helpString += "The cluster parameter allows you to indicate whether you want to run the clustering or just split the distance matrix, default=t";
helpString += "The cutoff parameter allow you to set the distance you want to cluster to, default is 0.25. \n";
helpString += "The precision parameter allows you specify the precision of the precision of the distances outputted, default=100, meaning 2 decimal places. \n";
- helpString += "The method allows you to specify what clustering algorythm you want to use, default=average, option furthest, nearest, or average. \n";
+ helpString += "The method allows you to specify what clustering algorithm you want to use, default=average, option furthest, nearest, or average. \n";
helpString += "The splitmethod parameter allows you to specify how you want to split your distance file before you cluster, default=distance, options distance, classify or fasta. \n";
helpString += "The taxonomy parameter allows you to enter the taxonomy file for your sequences, this is only valid if you are using splitmethod=classify. Be sure your taxonomy file does not include the probability scores. \n";
helpString += "The taxlevel parameter allows you to specify the taxonomy level you want to use to split the distance file, default=3, meaning use the first taxon in each list. \n";
m->mothurOutEndLine(); m->mothurOut("Clustering " + thisDistFile); m->mothurOutEndLine();
//create cluster
- if (method == "furthest") { cluster = new CompleteLinkage(rabund, list, matrix, cutoff, method); }
- else if(method == "nearest"){ cluster = new SingleLinkage(rabund, list, matrix, cutoff, method); }
- else if(method == "average"){ cluster = new AverageLinkage(rabund, list, matrix, cutoff, method); }
+ float adjust = -1.0;
+ if (method == "furthest") { cluster = new CompleteLinkage(rabund, list, matrix, cutoff, method, adjust); }
+ else if(method == "nearest"){ cluster = new SingleLinkage(rabund, list, matrix, cutoff, method, adjust); }
+ else if(method == "average"){ cluster = new AverageLinkage(rabund, list, matrix, cutoff, method, adjust); }
tag = cluster->getTag();
if (outputDir == "") { outputDir += m->hasPath(thisDistFile); }